All too frequently, the biosynthesis of a structurally defined and functional protein does not end with the termination of the growing polypeptide chain, but rather depends on subsequent protein processing events. The long-term goal of this research is to understand the origins of specificity and selectivity in protein co- and post-translational modification reactions. This objective presents a significant challenge because, in each covalent modification reaction the opportunities for competing transformations, on the densely functionalized protein substrate, are innumerable. Since enzyme-catalyzed protein derivatization is a key event in many biological control mechanisms, an understanding of the origin of specificity is of utmost importance both to fundamental biochemistry and to a consideration of the mechanisms of homeostatic control. Thus, protein processing and the complex issue of protein folding manifest themselves as presently insurmountable obstacles in the interpretation of genetic information. The focus of the research is to evaluate to what extent, and by what mechanisms, the inherent reactivity of specific amino acid side chain functionality is augmented as a result of the local polypeptide sequence in which it resides. Thus, the details of an in depth study of several protein processing reactions is presented. These include N-glycosylation of asparagine mediated by oligosaccharyl transferase, O-glycosylation of threonine and serine mediated by UDP-GalNAc: polypeptide GalNAc transferase and methylation of the acidic residues aspartic acid and glutamic acid and the basic amino acid side chains of lysine by methyltransferases II and III respectively. The experimental approach in this investigation is multidisciplinary, involving the development of methods for establishing sequence specificity patterns, conformational and kinetic analyses of ideal peptidyl substrates and construction of conformationally defined substrates to substantiate any proposed model. Based on a knowledge of the important non-covalent interactions that prevail in a particular transformation, research can proceed to the design nd synthesis of both transition state analogs and affinity labelling agents which are targeted to probe the validity of any mechanistic proposal. Integral to this research are studies on the purification and structural characterization of the enzymes involved in each transformation.